add test_data

input_files/group.txt

+GRP1;z_GIANT_HEIGHT z_GIANT_BMI

input_files/test_meta.csv

+filename	internalDataLink	Consortium	Outcome	FullName	Type	Reference	ReferenceLink	dataLink	Nsample	Ncase	Ncontrol	Nsnp	snpid	a1	a2	freq	pval	n	z	OR	se	code	imp	ncas	ncont	altNcas	altNcont	Unnamed: 28
+GIANT_HEIGHT_Wood_et_al_2014_publicrelease_HapMapCeuFreq.txt		GIANT	HEIGHT	Height	Anthropometry	Wood et al. 2014	http://www.ncbi.nlm.nih.gov/pubmed/25282103	https://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files 	253288			2550858.0	MarkerName	Allele1	Allele2	Freq.Allele1.HapMapCEU	p	N	b		SE
+SNP_gwas_mc_merge_nogc.tbl.uniq		GIANT	BMI	Body Mass Index	Anthropometry	Locke et al. 2015	http://www.ncbi.nlm.nih.gov/pubmed/25673413	https://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files 	339224			2554637.0	SNP	A1	A2	Freq1.Hapmap	p	N	b		se

nextflow.config

@@ -25,7 +25,7 @@ process{
         maxRetries=3
         maxForks=400
         queueSize=500
-        errorStrategy='retry'
+        errorStrategy='finish'
         cache='deep'
 
 

nextflow_local.config

+dag {
+    enabled = true
+    file = 'dag.dot'
+}
+
+report {
+       enabled = true
+       file = 'nextflow_logs/report.html'
+}
+
+trace {
+        enabled = true
+        file = 'nextflow_logs/trace.txt'
+}
+
+singularity {
+            enabled = true
+            autoMounts = true
+            runOptions = '--home $HOME:/home/$USER'
+}
+
+process{
+        executor='local'
+        maxErrors=10
+        maxRetries=3
+        maxForks=400
+        queueSize=500
+        errorStrategy='retry'
+        cache='deep'
+
+
+    withName: 'Compute_MAF' {
+        container='docker://quay.io/biocontainers/plink_1.90b5--heea4ae3_0'
+        cpus=1
+        }
+
+    withName: 'create_WG_reference_panel' {
+		container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
+		cpus=1
+	}
+
+    withName: 'meta_data_GWAS' {
+        cpus=1
+    }
+
+    withName: 'Clean_GWAS' {
+        container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
+        cpus=1
+    }
+
+    withName: 'Impute_GWAS' {
+      container="docker://quay.io/biocontainers/raiss_2.0--py_0"
+        cpus=1
+    }
+
+    withName: 'Munge_LDSC_data' {
+      container='docker://quay.io/biocontainers/ldsc_1.0.1--py_0'
+        cpus=1
+    }
+
+    withName: 'Generate_trait_pair' {
+    container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
+    cpus=1
+    }
+
+    withName: 'Correlation_LDSC_data' {
+      container="docker://quay.io/biocontainers/ldsc_1.0.1--py_0.sif"
+        cpus=1
+    }
+
+    withName: 'Correlation_matrices' {
+      container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
+        cpus=1
+    }
+
+    withName: 'Create_inittable_LDSC' {
+      container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
+        cpus=1
+    }
+
+    withName: 'Create_inittable' {
+      container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
+        cpus=1
+    }
+
+    withName: 'get_pheno_group' {
+        cpus=1
+    }
+
+    withName: 'Create_project_data' {
+      container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
+        cpus=1
+    }
+
+}